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The Joys and Perils of Flexible Fitting

  • Niels VolkmannEmail author
Chapter
Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 805)

Abstract

While performing their functions, biological macromolecules often form large, dynamically changing macromolecular assemblies. Only a relatively small number of such assemblies have been accessible to the atomic-resolution techniques X-ray crystallography and NMR. Electron microscopy in conjunction with image reconstruction has become the preferred alternative for revealing the structures of such macromolecular complexes. However, for most assemblies the achievable resolution is too low to allow accurate atomic modeling directly from the data. Yet, useful models often can be obtained by fitting atomic models of individual components into a low-resolution reconstruction of the entire assembly. Several algorithms for achieving optimal fits in this context were developed recently, many allowing considerable degrees of flexibility to account for binding-induced conformational changes of the assembly components. This chapter describes the advantages and potential pitfalls of these methods and puts them into perspective with alternative approaches such as iterative modular fitting of rigid-body domains.

Keywords

Electron microscopy Fitting Validation Statistical methods Modeling 

Notes

Acknowledgements

This work was supported by National Institutes of Health grant P01 GM066311.

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© Springer International Publishing Switzerland 2014

Authors and Affiliations

  1. 1.Bioinformatics and Systems Biology ProgramSanford-Burnham Medical Research InstituteLa JollaUSA

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